title: ChIP-Seq analysis of H3K27me3 in Mobilized CD34 cells; Lib:RI:20100603:11--ChIP:MA:20100517:11:Mobilized CD34:H3K27Me3

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100603:11--ChIP:MA:20100517:11:Mobilized CD34:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7513
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2422
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM773047_BI.Mobilized_CD34_Primary_Cells.H3K27me3.RO_01562.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100603:11--ChIP:MA:20100517:11:Mobilized CD34:H3K27Me3.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01562 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8226
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,884,197
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.2782
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2973
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9878
IROC_PERCENTILE: 91
POISSON_SCORE: 0.4944
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.95

**********************************************************************

ANALYSIS FILE NAME: GSM773047_BI.Mobilized_CD34_Primary_Cells.H3K27me3.RO_01562.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100603:11--ChIP:MA:20100517:11:Mobilized CD34:H3K27Me3.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01562 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8253
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: MCD34 H3K27me3 62
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K27me3 Donor RO 01562 Library Lib:RI:20100603:11--ChIP:MA:20100517:11:Mobilized Mobilized CD34:H3K27Me3 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,884,197
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.2782
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2973
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9878
IROC_PERCENTILE: 91
POISSON_SCORE: 0.4944
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.95

**********************************************************************

source_name: flow sorted CD34+ cells from cord blood; Lib:RI:20100603:11--ChIP:MA:20100517:11:Mobilized CD34:H3K27Me3

value: CD34 Primary Cells

value: genomic DNA

tag: disease

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: 42 years

value: Male

value: Caucasian

value: Histone H3K27me3


title: Lung_asthmatic_post-placebo (SRC117240)

status: Public on Jan 18 2011

type: RNA

city: South San Francisco

first: Alex

last: Abbas

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc.

description:
Lung biopsy from placebo treated asthmatic, post-treatment
SRC117240

hyb_protocol: 18 hours at 60°C with constant rotation on Agilent WHG

scan_protocol: Agilent scanner according to the manufacturer’s protocol

data_processing: the data were extracted and normalized according to the default settings of Agilent Feature Extraction 7.5. LOWESS normalization, background subtraction, and ratio computation.

molecule: total RNA

organism: Homo sapiens

label_protocol: T7 RNA polymerase single round of linear amplification

extract_protocol: micro total RNA isolation from animal tissues protocol (Qiagen, Valencia, CA)

tag: age

tag: Sex

value: F

tag: batch

tag: disease state

value: Asthma

tag: patientid

tag: th2 signature

value: High

tag: time

value: post-treatment

tag: treatment protocol

value: Placebo

source_name: Stratagene Universal Human Reference

tag: reference

value: Stratagene Universal Human Reference


title: Lung_healthy (SRC119795)

description:
Lung biopsy from healthy control
SRC119795

source_name: human lung biopsy_healthy

value: Healthy

value: control

value: no treatment


title: Lung_healthy (SRC119773)

description:
Lung biopsy from healthy control
SRC119773

value: M


title: Lung_asthmatic_post-flovent (SRC117326)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117326

value: Low

value: Flovent


title: ChIP-Seq analysis of H3K4me3 in HUES48 cells; Lib:MC:20101025:08--ChIP:MC:20101020:08:ES cell HUES_48:H3K4Me3

status: Public on Mar 31 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20101025:08--ChIP:MC:20101020:08:ES cell HUES_48:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5677
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5930
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669936_BI.HUES48.H3K4me3.Lib_MC_20101025_08--ChIP_MC_20101020_08_ES_cell_HUES_48_H3K4Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:08--ChIP:MC:20101020:08:ES cell HUES_48:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES48 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the HUES48 Cell Line, Library Lib:MC:20101025:08--ChIP:MC:20101020:08:ES cell HUES_48:H3K4Me3 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6551
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.654
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.6495
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9984
IROC_PERCENTILE: 52
POISSON_SCORE: 0.6652
POISSON_PERCENTILE: 88

**********************************************************************

ANALYSIS FILE NAME: GSM669936_BI.HUES48.H3K4me3.Lib_MC_20101025_08--ChIP_MC_20101020_08_ES_cell_HUES_48_H3K4Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:08--ChIP:MC:20101020:08:ES cell HUES_48:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES48 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the HUES48 Cell Line, Library Lib:MC:20101025:08--ChIP:MC:20101020:08:ES cell HUES_48:H3K4Me3 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6761
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES48 H3K4me3 e3
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line Histone H3K4me3 Library Lib:MC:20101025:08--ChIP:MC:20101020:08:ES cell HUES_48:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.654
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.6495
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9984
IROC_PERCENTILE: 52
POISSON_SCORE: 0.6652
POISSON_PERCENTILE: 88

**********************************************************************

molecule: genomic DNA

source_name: Harvard University Embryonic Stem Cells; Lib:MC:20101025:08--ChIP:MC:20101020:08:ES cell HUES_48:H3K4Me3

extract_protocol: Library construction protocol: Single read - Illumina

value: HUES48 stem cells

tag: sample alias

tag: sample common name

value: HUES48 Cell Line

tag: lineage

value: embrionic stem cell

tag: medium

value: KSR

tag: molecule

value: genomic DNA

tag: passage

tag: line

value: ES cell HUES_48-1

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Bioruptor


title: Lung_asthmatic_post-flovent (SRC117252)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117252

value: F

value: Asthma

value: Low

value: post-treatment

value: Flovent

value: Stratagene Universal Human Reference


title: ChIP-Seq analysis of H3K4me3 in HUES64 cells; Lib:MC:20101025:02--ChIP:MC:20101020:02:ES cell HUES_64:H3K4Me3

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20101025:02--ChIP:MC:20101020:02:ES cell HUES_64:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5708
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5931
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669967_BI.HUES64.H3K4me3.Lib_MC_20101025_02--ChIP_MC_20101020_02_ES_cell_HUES_64_H3K4Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:02--ChIP:MC:20101020:02:ES cell HUES_64:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES64 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the HUES64 Cell Line, Library Lib:MC:20101025:02--ChIP:MC:20101020:02:ES cell HUES_64:H3K4Me3 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6452
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.6568
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.6513
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9983
IROC_PERCENTILE: 44
POISSON_SCORE: 0.6758
POISSON_PERCENTILE: 92

**********************************************************************

ANALYSIS FILE NAME: GSM669967_BI.HUES64.H3K4me3.Lib_MC_20101025_02--ChIP_MC_20101020_02_ES_cell_HUES_64_H3K4Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:02--ChIP:MC:20101020:02:ES cell HUES_64:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the HUES64 Cell Line, Library Lib:MC:20101025:02--ChIP:MC:20101020:02:ES cell HUES_64:H3K4Me3 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6662
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES64 H3K4me3 e3
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K4me3 Library Lib:MC:20101025:02--ChIP:MC:20101020:02:ES cell HUES_64:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.6568
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.6513
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9983
IROC_PERCENTILE: 44
POISSON_SCORE: 0.6758
POISSON_PERCENTILE: 92

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib:MC:20101025:02--ChIP:MC:20101020:02:ES cell HUES_64:H3K4Me3

value: HUES64 Cell Line

value: embrionic stem cell

value: KSR

value: genomic DNA

tag: disease

value: ES cell HUES_64-1

value: Cell Line


title: Lung_asthmatic_post-flovent (SRC117307)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117307

tag: age

value: M

value: High


title: Lung_asthmatic_pre-placebo (SRC117163)

description:
Lung biopsy from placebo treated asthmatic, pre-treatment
SRC117163

source_name: human lung biopsy_asthmatic_pre-placebo

tag: Sex

value: pre-treatment

value: Placebo


title: Lung_asthmatic_pre-placebo (SRC117136)

description:
Lung biopsy from placebo treated asthmatic, pre-treatment
SRC117136

tag: batch


title: Lung_asthmatic_pre-placebo (SRC117361)

description:
Lung biopsy from placebo treated asthmatic, pre-treatment
SRC117361

tag: disease state


title: ChIP-Seq analysis of WCE in HUES 6 cells; Lib:XZ:20101004:07--ChIP:XZ:20100930:07:ES cell HUES_6:WCE

description:
sample_term_id: NTR_0000841
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20101004:07--ChIP:XZ:20100930:07:ES cell HUES_6:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5617
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5642
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669888_BI.HUES6.Input.Lib_XZ_20101004_07--ChIP_XZ_20100930_07_ES_cell_HUES_6_WCE.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:07--ChIP:XZ:20100930:07:ES cell HUES_6:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES6 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the HUES6 Cell Line, Library Lib:XZ:20101004:07--ChIP:XZ:20100930:07:ES cell HUES_6:WCE were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6569
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0197
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0507
POISSON_PERCENTILE: 40

**********************************************************************

ANALYSIS FILE NAME: GSM669888_BI.HUES6.Input.Lib_XZ_20101004_07--ChIP_XZ_20100930_07_ES_cell_HUES_6_WCE.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:07--ChIP:XZ:20100930:07:ES cell HUES_6:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES6 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the HUES6 Cell Line, Library Lib:XZ:20101004:07--ChIP:XZ:20100930:07:ES cell HUES_6:WCE were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6779
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES6 Input CE.1
BROWSER_TRACK_DESCRIPTION: BI HUES6 Cell Line ChIP-Seq Input Library Lib:XZ:20101004:07--ChIP:XZ:20100930:07:ES cell HUES_6:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0197
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0507
POISSON_PERCENTILE: 40

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib:XZ:20101004:07--ChIP:XZ:20100930:07:ES cell HUES_6:WCE

value: HUES6 Cell Line

value: HUES 6

value: ES cell HUES_6-1

value: undifferentiated

value: Unknown

value: Harvard University

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: Lung_asthmatic_post-flovent (SRC117285)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117285

value: F

value: Asthma

tag: patientid

value: Low

value: post-treatment

value: Flovent

value: Stratagene Universal Human Reference


title: Lung_asthmatic_post-flovent (SRC117312)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117312

value: M

tag: th2 signature

value: High


title: Lung_asthmatic_pre-flovent (SRC117181)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117181

source_name: human lung biopsy_asthmatic_pre-flovent

tag: time

value: pre-treatment


title: Lung_asthmatic_post-placebo (SRC117218)

description:
Lung biopsy from placebo treated asthmatic, post-treatment
SRC117218

tag: treatment protocol

value: Placebo


title: Lung_asthmatic_pre-placebo (SRC117352)

description:
Lung biopsy from placebo treated asthmatic, pre-treatment
SRC117352

tag: reference


title: Lung_asthmatic_pre-placebo (SRC117207)

description:
Lung biopsy from placebo treated asthmatic, pre-treatment
SRC117207


title: Lung_asthmatic_pre-flovent (SRC117261)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117261


title: Lung_asthmatic_pre-placebo (SRC117150)

description:
Lung biopsy from placebo treated asthmatic, pre-treatment
SRC117150


title: Lung_healthy (SRC119786)

description:
Lung biopsy from healthy control
SRC119786

value: Healthy

value: control

value: no treatment


title: Lung_healthy (SRC119835)

description:
Lung biopsy from healthy control
SRC119835


title: Lung_healthy (SRC119809)

description:
Lung biopsy from healthy control
SRC119809


title: Lung_healthy (SRC119758)

description:
Lung biopsy from healthy control
SRC119758


title: Lung_asthmatic_post-flovent (SRC117233)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117233


title: Lung_asthmatic_pre-flovent (SRC117293)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117293


title: Lung_asthmatic_pre-placebo (SRC117185)

description:
Lung biopsy from placebo treated asthmatic, pre-treatment
SRC117185


title: Lung_asthmatic_pre-flovent (SRC117282)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117282


title: Lung_asthmatic_post-flovent (SRC117245)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117245


title: Lung_asthmatic_pre-flovent (SRC117143)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117143


title: Lung_asthmatic_post-flovent (SRC117344)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117344


title: Lung_asthmatic_post-placebo (SRC117131)

description:
Lung biopsy from placebo treated asthmatic, post-treatment
SRC117131


title: Lung_asthmatic_post-placebo (SRC117292)

description:
Lung biopsy from placebo treated asthmatic, post-treatment
SRC117292


title: Lung_asthmatic_pre-flovent (SRC117168)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117168


title: Lung_asthmatic_post-flovent (SRC117222)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117222


title: Lung_asthmatic_pre-placebo (SRC117201)

description:
Lung biopsy from placebo treated asthmatic, pre-treatment
SRC117201


title: Lung_asthmatic_pre-flovent (SRC117153)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117153


title: Lung_asthmatic_pre-placebo (SRC117156)

description:
Lung biopsy from placebo treated asthmatic, pre-treatment
SRC117156


title: Lung_asthmatic_post-flovent (SRC117230)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117230


title: Lung_healthy (SRC119828)

description:
Lung biopsy from healthy control
SRC119828


title: Lung_asthmatic_pre-flovent (SRC117315)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117315


title: Lung_asthmatic_pre-placebo (SRC117193)

description:
Lung biopsy from placebo treated asthmatic, pre-treatment
SRC117193


title: Lung_healthy (SRC119803)

description:
Lung biopsy from healthy control
SRC119803


title: Lung_asthmatic_post-flovent (SRC117303)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117303


title: Lung_asthmatic_pre-flovent (SRC117176)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117176


title: Lung_asthmatic_pre-flovent (SRC117171)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117171


title: Lung_asthmatic_pre-flovent (SRC117330)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117330


title: Lung_asthmatic_post-flovent (SRC117340)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117340


title: Lung_healthy (SRC119816)

description:
Lung biopsy from healthy control
SRC119816


title: Lung_asthmatic_pre-flovent (SRC117190)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117190


title: Lung_healthy (SRC119766)

description:
Lung biopsy from healthy control
SRC119766


title: Lung_asthmatic_post-placebo (SRC117225)

description:
Lung biopsy from placebo treated asthmatic, post-treatment
SRC117225


title: CY88_3_G04_S652_comb

status: Public on Apr 05 2016

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

description: single cell RNA-seq

library_source: transcriptomic

data_processing:
Following sequencing on the NextSeq, BAM files were converted to merged, demultiplexed FASTQs. Paired-end reads were then mapped to the UCSC hg19 human transcriptome using Bowtie with parameters "-q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 -S -p 6", which allows alignment of sequences with single base changes such as due to point mutations. Expression levels of genes were quantified as Ei,j=log2(TPMi,j/10+1), where TPMi,j refers to transcript-per-million (TPM) for gene i in sample j, as calculated by RSEM v1.2.3 in paired-end mode. TPM values were divided by 10 since we estimate the complexity of our single cell libraries to be on the order of 100,000 transcripts and would like to avoid counting each transcript ~10 times, as would be the case with TPM, which may inflate the difference between the expression level of a gene in cells in which the gene is detected and those in which it is not detected. For each cell, we quantified the number of genes for which at least one read was mapped, and the average expression level of a curated list of housekeeping genes. We then excluded all cells with either fewer than 1,700 detected genes or an average housekeeping expression (E, as defined above) below 3. Only genes detected with E>2 in at least 5 cells were retained in the processed data file.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing the normalized expression levels (E) for all genes with E>2 in at least 5 cells, across 3,249 cells that passed QC. the tumor-of-origin is indicated in the name of each cell (CY##). The first row denotes the classification (based on inferred CNVs) to malignant (2), non-malignant (1) or unresolved (0) cells. The second row denotes the inferred cell types for non-malignant cells, including T-cells (1), B-cells (2), Macrophages (3), Endothelial cells (4) and CAFs (5). All other rows correspond to genes.

molecule: polyA RNA

source_name: melanoma tumor

growth_protocol: no culturing (freshly-resected tumor samples)

extract_protocol:
RNA and DNA were isolated using the Qiagen minikit following the manufacturers recommendations.  Whole Transcriptome amplification (WTA) was performed with a modified SMART-Seq2 protocol, with Maxima Reverse Transcriptase (Life Technologies) used in place of superscript II.
WTA products were cleaned with Agencourt XP DNA beads and 70% ethanol (Beckman Coulter) and Illumina sequencing libraries were prepared using Nextera XT (Illumina), as previously described (15). The 96 samples of a multiwall plate were pooled together, and cleaned with two 0.8x DNA SPRIs (Beckman Coulter). Library quality was assessed with a high sensitivity DNA chip (Agilent) and quantified with a high sensitivity dsDNA Quant Kit (Life Technologies). Samples were sequenced on an Illumina NextSeq 500 instrument using 30bp paired-end reads.

treatment_protocol: Resected tumors were transported in DMEM (ThermoFisher Scientific) on ice immediately after surgical procurement. Tumors were rinsed with PBS (Life Technologies). A small fragment was stored in RNA-protect (Qiagen) for bulk RNA and DNA isolation. Using scalpels, the remainder of the tumor was minced into tiny cubes <1 mm3 and transferred into a 50 ml conical tube (BD Falcon) containing 10 ml pre-warmed M199-media (ThermoFisher Scientific), 2 mg/ml collagenase P (Roche) and 10U/μl DNase I (Roche). Tumor pieces were digested in this digestion media for 10 minutes at 37°C, then vortexed for 10 seconds and pipetted up and down for 1 minute using pipettes of descending sizes (25 ml, 10 ml and 5 ml). If needed, this was repeated twice more until a single-cell suspension was obtained. This suspension was then filtered using a 70μm mesh (ThermoFisher Scientific) and residual cell clumps were discarded. The suspension was supplemented with 30 ml PBS (Life Technologies) with 2% fetal calf serum (FCS) (Gemini Bioproducts) and immediately placed on ice. After centrifuging at 580g at 4°C for 6 minutes, the supernatant was discarded and the cell pellet was re-suspended in PBS with FCS and placed on ice prior to staining for FACS. Single-cell suspensions were stained with CD45-FITC (VWR), Calcein-AM (Life Technologies) and CD90-PE (BioLegend) per manufacturer recommendations. First, doublets were excluded based on forward and sideward scatter, then we gated on viable cells (Calceinhigh) and sorted single cells (CD45+ or CD45-CD90+ or CD45-CD90-) into 96-well plates chilled to 4°C, pre-prepared with 10μl TCL buffer (Qiagen) supplemented with 1% beta-mercaptoethanol (lysis buffer). Single-cell lysates were vortexed, spun down at 3700 rpm at 4°C for 2 minutes, immediately placed on dry ice and transferred for storage at -80°C.

tag: tumor-of-origin


title: Lung_asthmatic_post-placebo (SRC117320)

description:
Lung biopsy from placebo treated asthmatic, post-treatment
SRC117320


title: Lung_asthmatic_post-flovent (SRC117237)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117237


title: Lung_asthmatic_pre-placebo (SRC117347)

description:
Lung biopsy from placebo treated asthmatic, pre-treatment
SRC117347


title: Lung_healthy (SRC119812)

description:
Lung biopsy from healthy control
SRC119812


title: Lung_healthy (SRC119778)

description:
Lung biopsy from healthy control
SRC119778


title: Lung_asthmatic_pre-flovent (SRC117196)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117196


title: Lung_healthy (SRC119821)

description:
Lung biopsy from healthy control
SRC119821


title: Lung_asthmatic_post-flovent (SRC117212)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117212


title: ChIP-Seq analysis of H3K27me3; mobilized CD34 cells; Lib:RI:20100517:06--ChIP:Thanh:20100504:06:Mobilized CD34:H3K27Me3

status: Public on Nov 12 2010

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100517:06--ChIP:Thanh:20100504:06:Mobilized CD34:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3248
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3352
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621664_BI.Mobilized_CD34_Primary_Cells.H3K27me3.UW_RO_01536.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:06--ChIP:Thanh:20100504:06:Mobilized CD34:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01536 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4620
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0576
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1353
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.8972
IROC_PERCENTILE: 42
POISSON_SCORE: 0.3316
POISSON_PERCENTILE: 6

**********************************************************************

ANALYSIS FILE NAME: GSM621664_BI.Mobilized_CD34_Primary_Cells.H3K27me3.UW_RO_01536.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:06--ChIP:Thanh:20100504:06:Mobilized CD34:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01536 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4894
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 H3K27me3 36
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K27me3 Donor RO 01536 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0576
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1353
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.8972
IROC_PERCENTILE: 42
POISSON_SCORE: 0.3316
POISSON_PERCENTILE: 6

**********************************************************************

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100517:06--ChIP:Thanh:20100504:06:Mobilized CD34:H3K27Me3

value: genomic DNA

tag: markers

value: Mobilized CD34

value: Hisp

value: Female

value: Primary Cell

value: UW

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K4me3 in mobilized CD34 cells; Lib:RI:20100517:03--ChIP:Thanh:20100504:03:Mobilized CD34:H3K4Me3

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100517:03--ChIP:Thanh:20100504:03:Mobilized CD34:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3249
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3352
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621665_BI.Mobilized_CD34_Primary_Cells.H3K4me3.UW_RO_01536.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:03--ChIP:Thanh:20100504:03:Mobilized CD34:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01536 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4577
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.2233
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.2531
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3317
POISSON_PERCENTILE: 8

**********************************************************************

ANALYSIS FILE NAME: GSM621665_BI.Mobilized_CD34_Primary_Cells.H3K4me3.UW_RO_01536.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:03--ChIP:Thanh:20100504:03:Mobilized CD34:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01536 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4851
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 H3K4me3 36
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me3 Donor RO 01536 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.2233
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.2531
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3317
POISSON_PERCENTILE: 8

**********************************************************************

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100517:03--ChIP:Thanh:20100504:03:Mobilized CD34:H3K4Me3

value: Histone H3K4me3

value: Bioruptor


title: ChIP-Seq analysis of H3K27me3 in Mobilized CD34 cells; Lib:RI:20100524:13--ChIP:MA:20100517:13:Mobilized CD34:H3K27Me3

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100524:13--ChIP:MA:20100517:13:Mobilized CD34:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3771
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3881
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621431_BI.Mobilized_CD34_Primary_Cells.H3K27me3.UW_RO_01549.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:13--ChIP:MA:20100517:13:Mobilized CD34:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01549 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4595
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.249
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.2998
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9651
IROC_PERCENTILE: 79
POISSON_SCORE: 0.5241
POISSON_PERCENTILE: 73

**********************************************************************

ANALYSIS FILE NAME: GSM621431_BI.Mobilized_CD34_Primary_Cells.H3K27me3.UW_RO_01549.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:13--ChIP:MA:20100517:13:Mobilized CD34:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01549 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4869
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 H3K27me3 49
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K27me3 Donor RO 01549 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.249
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.2998
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9651
IROC_PERCENTILE: 79
POISSON_SCORE: 0.5241
POISSON_PERCENTILE: 73

**********************************************************************

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100524:13--ChIP:MA:20100517:13:Mobilized CD34:H3K27Me3

value: Cauc


title: ChIP-Seq analysis of WCE in human Mobilized CD34 cells; Lib:RI:20100524:08--ChIP:MA:20100517:08:Mobilized CD34:WCE

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100524:08--ChIP:MA:20100517:08:Mobilized CD34:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3754
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3881
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621414_BI.Mobilized_CD34_Primary_Cells.Input.UW_RO_01549.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:08--ChIP:MA:20100517:08:Mobilized CD34:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Mobilized CD34 Primary Cells, Donor RO 01549 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4760
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0065
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0042
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2414
POISSON_PERCENTILE: 60

**********************************************************************

ANALYSIS FILE NAME: GSM621414_BI.Mobilized_CD34_Primary_Cells.Input.UW_RO_01549.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:08--ChIP:MA:20100517:08:Mobilized CD34:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Mobilized CD34 Primary Cells, Donor RO 01549 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5034
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 Input 49
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells ChIP-Seq Input Donor RO 01549 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0065
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0042
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2414
POISSON_PERCENTILE: 60

**********************************************************************

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100524:08--ChIP:MA:20100517:08:Mobilized CD34:WCE

value: standard

value: ChIP-Seq Input

value: Input


title: Reference Epigenome: ChIP-Seq Input from hESC H1 Cells; renlab.Input.hESC-03.01

status: Public on Oct 07 2010

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
Design description: ChIP-Seq Input from hESC H1 Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL208
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3717
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3459
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM605335_UCSD.H1.Input.YL208.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the H1 Cell Line, Library YL208 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4427
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0889
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.083
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.4703
IROC_PERCENTILE: 34
POISSON_SCORE: 0.2829
POISSON_PERCENTILE: 72

**********************************************************************

ANALYSIS FILE NAME: GSM605335_UCSD.H1.Input.YL208.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 Cell Line, Library YL208 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4454
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 Input 08
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line ChIP-Seq Input Library YL208 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0889
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.083
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.4703
IROC_PERCENTILE: 34
POISSON_SCORE: 0.2829
POISSON_PERCENTILE: 72

**********************************************************************

source_name: Human embryonic stem cells; H1 cell line; renlab.Input.hESC-03.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

tag: lineage

value: Embryonic Stem Cell

value: mTeSER

value: Male

value: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Input from hESC H1 Cells; renlab.Input.hESC-07.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from hESC H1 Cells. Sequencing was done on the Illumina GAII platform.
Library name: LLH1U
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3725
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM605339_UCSD.H1.Input.LLH1U.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-07.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the H1 Cell Line, Library LLH1U were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4399
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0209
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.187
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.7755
IROC_PERCENTILE: 48
POISSON_SCORE: 0.2048
POISSON_PERCENTILE: 34

**********************************************************************

ANALYSIS FILE NAME: GSM605339_UCSD.H1.Input.LLH1U.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-07.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 Cell Line, Library LLH1U were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4469
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 Input 1U
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line ChIP-Seq Input Library LLH1U EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0209
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.187
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.7755
IROC_PERCENTILE: 48
POISSON_SCORE: 0.2048
POISSON_PERCENTILE: 34

**********************************************************************

source_name: Human embryonic stem cells; H1 cell line; renlab.Input.hESC-07.01

value: Between 20 and 40

tag: medium

value: Branson Tip Sonicator


title: ChIP-Seq analysis of H3K4me3 in Mobilized CD34 cells; Lib:RI:20100524:03--ChIP:MA:20100517:03:Mobilized CD34:H3K4Me3

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100524:03--ChIP:MA:20100517:03:Mobilized CD34:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3744
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3894
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621404_BI.Mobilized_CD34_Primary_Cells.H3K4me3.UW_RO_01517.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:03--ChIP:MA:20100517:03:Mobilized CD34:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01517 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4624
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.5009
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.5403
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5578
POISSON_PERCENTILE: 66

**********************************************************************

ANALYSIS FILE NAME: GSM621404_BI.Mobilized_CD34_Primary_Cells.H3K4me3.UW_RO_01517.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:03--ChIP:MA:20100517:03:Mobilized CD34:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01517 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4898
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 H3K4me3 17
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me3 Donor RO 01517 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.5009
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.5403
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5578
POISSON_PERCENTILE: 66

**********************************************************************

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100524:03--ChIP:MA:20100517:03:Mobilized CD34:H3K4Me3

tag: molecule

value: Mobilized CD34

value: Unknown

value: Primary Cell

value: UW

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in hESC Cells; renlab.H3K4me3.hESC-03.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: SAK67
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3555
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM605315_UCSD.H1.H3K4me3.SAK67.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.hESC-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the H1 Cell Line, Library SAK67 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4409
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.7381
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.6969
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7086
POISSON_PERCENTILE: 87

**********************************************************************

ANALYSIS FILE NAME: GSM605315_UCSD.H1.H3K4me3.SAK67.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.hESC-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the H1 Cell Line, Library SAK67 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4536
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K4me3 67
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K4me3 Library SAK67 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.7381
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.6969
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7086
POISSON_PERCENTILE: 87

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K4me3.hESC-03.01

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

tag: passage

value: Histone H3K4me3

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore 04-745


title: ChIP-Seq analysis of WCE in human hES I3 TESR cells; Lib:MC:20090522:07--ChIP:MC:20090519:07:hES I3 TESR:WCE

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20090522:07--ChIP:MC:20090519:07:hES I3 TESR:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3158
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3160
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM621386_BI.ES-I3.Input.Lib_MC_20090522_07--ChIP_MC_20090519_07_hES_I3_TESR_WCE.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20090522:07--ChIP:MC:20090519:07:hES I3 TESR:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of ES-I3 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the ES-I3 Cell Line, Library Lib:MC:20090522:07--ChIP:MC:20090519:07:hES I3 TESR:WCE were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4743
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0024
FINDPEAKS_PERCENTILE: 1
HOTSPOT_SCORE: 0.008
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2422
POISSON_PERCENTILE: 63

**********************************************************************

ANALYSIS FILE NAME: GSM621386_BI.ES-I3.Input.Lib_MC_20090522_07--ChIP_MC_20090519_07_hES_I3_TESR_WCE.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20090522:07--ChIP:MC:20090519:07:hES I3 TESR:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-I3 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the ES-I3 Cell Line, Library Lib:MC:20090522:07--ChIP:MC:20090519:07:hES I3 TESR:WCE were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5017
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESI3 Input CE
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line ChIP-Seq Input Library Lib:MC:20090522:07--ChIP:MC:20090519:07:hES I3 TESR:WCE EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0024
FINDPEAKS_PERCENTILE: 1
HOTSPOT_SCORE: 0.008
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2422
POISSON_PERCENTILE: 63

**********************************************************************

source_name: I3 (eye three) stem cells; Lib:MC:20090522:07--ChIP:MC:20090519:07:hES I3 TESR:WCE

value: embrionic stem cell

value: TESR

tag: line

value: hES I3 TESR

value: hES I3 TESR-1

value: undifferentiated

value: Female

value: Harvard University

value: standard

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3 in human H1 cells; 30H81AAXX090613-8-S

status: Public on Apr 28 2010

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12522
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2496
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2353
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM537681_BI.H1.H3K4me3.Solexa-12522.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H81AAXX090613-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the H1 Cell Line, Library Solexa-12522 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4603
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.2333
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.2734
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3145
POISSON_PERCENTILE: 5

**********************************************************************

ANALYSIS FILE NAME: GSM537681_BI.H1.H3K4me3.Solexa-12522.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H81AAXX090613-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the H1 Cell Line, Library Solexa-12522 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4877
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K4me3 22
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line Histone H3K4me3 Library Solexa-12522 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.2333
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.2734
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3145
POISSON_PERCENTILE: 5

**********************************************************************

source_name: H1 stem cells from Cellular Dynamics; 30H81AAXX090613-8-S

value: genomic DNA

tag: disease

value: Cellular Dynamics

tag: sex

value: Male

value: SDS lysis

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Millipore


title: ChIP-Seq analysis of H3K27me3 in human hES-I3 cells; 314MFAAXX090227-8-S

status: Public on May 03 2010

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-10213/Solexa-15380
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2134
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2133
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM537648_BI.ES-I3.H3K27me3.Solexa-10213-15380.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314MFAAXX090227-8-S-42MNCAAXX100106-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-I3 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the ES-I3 Cell Line, Library Solexa-10213-15380 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4833
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.3673
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.3761
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9678
IROC_PERCENTILE: 83
POISSON_SCORE: 0.4786
POISSON_PERCENTILE: 60

**********************************************************************

ANALYSIS FILE NAME: GSM537648_BI.ES-I3.H3K27me3.Solexa-10213-15380.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314MFAAXX090227-8-S-42MNCAAXX100106-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-I3 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the ES-I3 Cell Line, Library Solexa-10213-15380 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5107
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESI3 H3K27me3 80
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line Histone H3K27me3 Library Solexa-10213 and Solexa-15380 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.3673
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.3761
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9678
IROC_PERCENTILE: 83
POISSON_SCORE: 0.4786
POISSON_PERCENTILE: 60

**********************************************************************

source_name: I3(eye three) stem cells; 314MFAAXX090227-8-S

value: Cell Line

value: embrionic stem cell

value: KSR

tag: Sex

value: Histone H3K27me3

value: Upstate or Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in hESC Cells; renlab.H3K27me3.hESC-03.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL95
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3545
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM605308_UCSD.H1.H3K27me3.YL95.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.hESC-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the H1 Cell Line, Library YL95 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4423
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2673
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.3196
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9143
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3913
POISSON_PERCENTILE: 31

**********************************************************************

ANALYSIS FILE NAME: GSM605308_UCSD.H1.H3K27me3.YL95.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.hESC-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the H1 Cell Line, Library YL95 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4537
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K27me3 95
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K27me3 Library YL95 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2673
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.3196
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9143
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3913
POISSON_PERCENTILE: 31

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K27me3.hESC-03.01

value: James Thompson Laboratory

value: Embryonic Stem Cell

value: Between 20 and 40

value: mTeSER

tag: batch

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: ChIP-Seq analysis of H3K27me3 in human H1 cells; 30H81AAXX090613-7-S

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12523
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2498
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2353
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM537683_BI.H1.H3K27me3.Solexa-12523.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H81AAXX090613-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the H1 Cell Line, Library Solexa-12523 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4584
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.3054
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.3386
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9753
IROC_PERCENTILE: 85
POISSON_SCORE: 0.4117
POISSON_PERCENTILE: 35

**********************************************************************

ANALYSIS FILE NAME: GSM537683_BI.H1.H3K27me3.Solexa-12523.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H81AAXX090613-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the H1 Cell Line, Library Solexa-12523 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4858
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K27me3 23
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line Histone H3K27me3 Library Solexa-12523 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.3054
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.3386
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9753
IROC_PERCENTILE: 85
POISSON_SCORE: 0.4117
POISSON_PERCENTILE: 35

**********************************************************************

source_name: H1 stem cells from Cellular Dynamics; 30H81AAXX090613-7-S

value: genomic DNA

value: Cellular Dynamics

value: undifferentiated

value: TESR

value: Male

value: SDS lysis

value: Bioruptor

value: 10 million cells


title: ChIP-Seq analysis of H3K27me3 in human hES I3 TESR cells; 30DUMAAXX090620-8-S

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12678
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2200
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2199
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM537627_BI.ES-I3.H3K27me3.Solexa-12678.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30DUMAAXX090620-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-I3 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the ES-I3 Cell Line, Library Solexa-12678 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4758
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1834
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.2653
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9768
IROC_PERCENTILE: 87
POISSON_SCORE: 0.3628
POISSON_PERCENTILE: 13

**********************************************************************

ANALYSIS FILE NAME: GSM537627_BI.ES-I3.H3K27me3.Solexa-12678.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30DUMAAXX090620-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-I3 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the ES-I3 Cell Line, Library Solexa-12678 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5032
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESI3 H3K27me3 78
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line Histone H3K27me3 Library Solexa-12678 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1834
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.2653
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9768
IROC_PERCENTILE: 87
POISSON_SCORE: 0.3628
POISSON_PERCENTILE: 13

**********************************************************************

source_name: I3(eye three) stem cells; 30DUMAAXX090620-8-S

value: Harvard University

value: Cell Line

value: hES I3 TESR

value: embrionic stem cell

value: Female

value: Histone H3K27me3

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Millipore


title: ChIP-Seq analysis of H3K4me3 in human hES-I3 cells; 42M0GAAXX091022-2-S

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-15474
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2170
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2169
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM537665_BI.ES-I3.H3K4me3.Solexa-15474.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42M0GAAXX091022-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-I3 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the ES-I3 Cell Line, Library Solexa-15474 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4714
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3815
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.3698
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9973
IROC_PERCENTILE: 27
POISSON_SCORE: 0.4454
POISSON_PERCENTILE: 45

**********************************************************************

ANALYSIS FILE NAME: GSM537665_BI.ES-I3.H3K4me3.Solexa-15474.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42M0GAAXX091022-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-I3 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the ES-I3 Cell Line, Library Solexa-15474 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4988
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESI3 H3K4me3 74
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line Histone H3K4me3 Library Solexa-15474 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3815
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.3698
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9973
IROC_PERCENTILE: 27
POISSON_SCORE: 0.4454
POISSON_PERCENTILE: 45

**********************************************************************

source_name: I3(eye three) stem cells; 42M0GAAXX091022-2-S

value: genomic DNA

value: KSR

value: Histone H3K4me3


title: ChIP-Seq analysis of WCE in human hES-I3 cells; 314MFAAXX090227-3-S

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-10219
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2188
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2187
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM537647_BI.ES-I3.Input.Solexa-10219.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314MFAAXX090227-3-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-I3 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the ES-I3 Cell Line, Library Solexa-10219 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4767
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.008
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.0959
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.4362
IROC_PERCENTILE: 31
POISSON_SCORE: 0.1941
POISSON_PERCENTILE: 24

**********************************************************************

ANALYSIS FILE NAME: GSM537647_BI.ES-I3.Input.Solexa-10219.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314MFAAXX090227-3-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-I3 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the ES-I3 Cell Line, Library Solexa-10219 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5041
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESI3 Input 19
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line ChIP-Seq Input Library Solexa-10219 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.008
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.0959
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.4362
IROC_PERCENTILE: 31
POISSON_SCORE: 0.1941
POISSON_PERCENTILE: 24

**********************************************************************

source_name: I3(eye three) stem cells; 314MFAAXX090227-3-S

value: undifferentiated

value: ChIP-Seq Input

value: Input

value: standard